I'm going through one of my cyclical interests in aircraft, so I thought this would be a good place to start collecting resources related to aircraft design.
Please feel free to add more, including on more esoteric topics. My practical experience is limited almost entirely to models and the like, so I tend to hove to a few simple rules which suit low-speed designs using props.
1. Basic principles
http://adg.stanford.edu/aa241/AircraftDesign.html
http://ocw.mit.edu/courses/aeronautics-and-astronautics/16-01-unified-engineering-i-ii-iii-iv-fall-2005-spring-2006/systems-labs-06/spl8.pdf
2. Wing and airfoil selection
http://www.wainfan.com/wingdes.pdf
http://airfoiltools.com/calculator/reynoldsnumber?MReNumForm%5Bvel%5D=60&MReNumForm%5Bchord%5D=1.5&MReNumForm%5Bkvisc%5D=1.5111E-5&yt0=Calculate
http://itlims.meil.pw.edu.pl/zsis/pomoce/BIPOL/BIPOL_1_handout_8A.pdf
http://m-selig.ae.illinois.edu/ads/aircraft.html
http://airfoiltools.com/search/index